Seventh Annual DOE Joint Genome Institute User Meeting Sponsored By U.S. Department of Energy Office of Science March 20-22, 2012 Walnut Creek Marriott Walnut Creek, California Contents Speaker Presentations .......................................................................................................... 1 Poster Presentations ........................................................................................................... 13 Attendees ............................................................................................................................ 83 Author Index ....................................................................................................................... 89 Speaker Presentations Abstracts alphabetical by speaker DOE Systems Biology Knowledgebase (Kbase) Adam Arkin ([email protected]) Lawrence Berkeley National Laboratory, Berkeley, California The Genome of Selaginella, a Remnant of an Ancient Vascular Plant Lineage Jody Banks ([email protected]) Botany and Plant Pathology, Purdue University, West Lafayette, Indiana Plants with lignified vascular tissues first appeared on earth about 400MY ago and subsequently diverged into several lineages. Only two of them remain: the euphyllophytes, which includes the ferns, gymnosperms and angiosperms, and the lycophytes. The genome sequence of the lycophyte Selaginella moellendorffii described here is the first lycophyte genome sequenced. Its compact genome, about two-thirds the size of Arabidopsis, has fewer genes with small intergenic regions and introns and no evidence of polyploidy. By comparing the Selaginella proteome with those of earlier diverging plants (Chlamydomonas and the moss Physcomitrella) and later diverging angiosperms, we were able to identify genes that coincide with the evolution of traits specific to land plants. Among these traits are vascular tissues consisting of special lignified cell types. Surprisingly, Selaginella produces an angiosperm-specific lignin. Recent studies indicate that the Selaginella lignin biosynthetic genes may be useful in modifying lignin in angiosperms. Genomics of Energy and the Environment Steven A. Benner ([email protected]) Foundation for Applied Molecular Evolution, The Westheimer Institute of Science and Technology, Gainesville, Florida The Earth and its biosphere co-evolve in tandem, each having influenced the other over the 4.5 billion year history of the planet. Genomic sequence data provide an important resource to explore and understand this co-evolution , especially if experimental methods are used to supplement theoretical modeling based on comparative sequence analysis. Paleogenetics provides experimental tools to address historical models based on genomic sequence analysis. Paleogenetics infers the sequences of ancestral genes and proteins from now-extinct organisms by analysis of the sequences of their descendents. Then, paleogenetics exploits recombinant DNA technology to bring these ancient biomolecules back to life, where they can be studied in the laboratory. This talk will describe the use of Abstracts alphabetical by speaker Speaker Presentations experimental paleogenetics to correlate the genomic, paleontological, and geological records of life on Earth. By resurrecting ancestral proteins from extinct organisms that lived long in the past, we can make broad statements about the chemistry behind adaptation, the nature of ancient environments, and the interaction between species in the ecosystem. We will start in the present day, and take steps back in time, first by 40 million years to the start of the most recent global climate deterioration, then back 100 million years to the age of the dinosaurs, and then back over 2 billion years, to the establishment of eubacteria on the planet. We will also discuss how this process if hindered by errors in modern genome sequence databases. Further, we will discuss the construction of "naturally organized" genome sequence databases, such as the MasterCatalog, which allow efficient organization, search, error correction and analysis, especially when compared with standard public genome sequence database. Getting to the Root of Things: Root Spatiotemporal Regulatory Networks Siobhan Brady ([email protected]) Genome Center, Department of Biology, College of Biological Sciences, University of California, Davis, Davis, California Plant root development provides a remarkably tractable system to delineate developmental gene regulatory networks and to study their functionality in a complex multicellular model system over developmental time. We present a gene regulatory network that regulates distinct transcriptional events in developmental time. Distinct regulatory modules were identified that temporally drive the expression of genes involved in xylem specification and in the subsequent synthesis of secondary cell wall metabolites associated with xylem differentiation. Reprogramming Bacteria to Seek and Destroy Small Molecules Justin P. Gallivan ([email protected]) Department of Chemistry and Center for Fundamental and Applied Molecular Evolution, Emory University, Atlanta, Georgia Simple organisms, such as the bacterium E. coli., carry out a wide variety of complex functions. E. coli cells synthesize complex molecules, communicate with one another, move in response to changing conditions, and replicate themselves every 20 minutes. The programs that control these behaviors are stored in a genome that encodes just over a megabyte of digital information. In this talk, I will present our recent efforts to reprogram E. coli to sense new small molecules and to respond to them with predictable behaviors. Specifically, I will describe our efforts to create synthetic riboswitches, which are designer RNA sequences that control gene expression in a ligand-dependent fashion without the need for proteins. I will show how synthetic riboswitches can be used to engineer bacteria to have a variety of functions, including the ability to seek and destroy small molecules, such as the herbicide atrazine. 2 Abstracts alphabetical by speaker Speaker Presentations The Evolution of Streamlined Genomes in Ocean Bacteria Stephen J. Giovannoni* ([email protected]) and J. Cameron Thrash Department of Microbiology, Oregon State University, Corvallis, Oregon The smallest genomes known from free-living cells are found in marine bacterioplankton. Genome sequences from cyanobacteria in the genus Prochlorococcus range in size from 1.6 - 2.7 Mbp. Genomes from heterotrophic cells in the SAR11 clade of Alphaproteobacteria are 1.3 - 1.5 Mbp. Genome sequences from obligate methylotrophs of the OM43 clade of Betaproteobacteria are 1.3 Mbp. Thus, in three metabolic categories, marine bacterioplankton hold the record for the smallest free-living genomes. Genome streamlining theory has been invoked to explain the small genomes of these cells. The essence of this theory is that selection is most efficient in microbial populations with large effective population sizes, and favors minimalism in the genomes and cell architecture of bacterioplankton because of selection for the efficient use of nutrient resources. Genome reduction also occurs in bacterial symbionts, where it has been attributed to genetic drift, and produces very different genomic signatures, including the expansion of non-coding genetic material, loss of anapleurotic pathways, and elevated rates of non-synonymous substitution. Comparative study of SAR11 genomes and experimental studies with cultures have revealed the metabolic consequences of genome streamlining. Most strains are deficient in assimilatory sulphate reduction and in normal pathways of glycine biosynthesis, making them dependent on organosulphur compounds and glycine, or glycine precursors, for growth. Many common regulatory systems are absent, and are replaced by simpler systems for maintaining cellular homeostasis, often involving riboswitches. Studies of ultrastructure and the metaproteomics of cells from oligotrophic oceans show that SAR11 have high surface-to-volume ratios and very high ratios of transport proteins, an apparent adaptation to enable efficient replication in ocean “deserts”. These observations support the broad conclusion that metabolic versatility has been sacrificed for simplicity and genome reduction in some bacterioplankton, rendering them able to use ambient nutrient resources efficiently but reducing their versatility. The question remains, how does the evolutionary history and ecology of these organisms differ from microbial plankton with genomes of average size? Systems Biology Approaches to Dissecting Plant Cell Wall Deconstruction in a Model Filamentous Fungus N. Louise Glass* ([email protected]), Sam Coradetti, Elizabeth Znameroski, Jianping Sun, James Craig, and Yi Yiong Plant and Microbial Biology Department, University of California, Berkeley, Berkeley, California Neurospora crassa colonizes burnt grasslands in the wild and metabolizes both cellulose and hemicellulose from plant cell walls. When switched from a favored carbon source such as sucrose to cellulose, N. crassa dramatically upregulates expression and secretion of a wide variety of genes encoding lignocellulolytic enzymes. However, the means by which N. crassa and other filamentous fungi sense the presence of cellulose in the environment remains unclear. In N. crassa, cellobiose efficiently induces cellulase gene expression in the absence of intra and Abstracts alphabetical by speaker 3 Speaker Presentations extracellular β-glucosidase